Increased robustness of form parsers.
This commit is contained in:
Landon Wark
@@ -6,7 +6,7 @@ import pprint
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from typing import List
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import pandas as pd
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from pathlib import Path
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from backend.db import models, lookup_kit_types, lookup_submission_type, lookup_samples
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from backend.db import models, lookup_kit_types, lookup_submission_type, lookup_samples, get_polymorphic_subclass
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from backend.pydant import PydSubmission, PydReagent
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import logging
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from collections import OrderedDict
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@@ -91,12 +91,11 @@ class SheetParser(object):
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Pulls basic information from the excel sheet
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"""
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info = InfoParser(ctx=self.ctx, xl=self.xl, submission_type=self.sub['submission_type']['value']).parse_info()
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parser_query = f"parse_{self.sub['submission_type']['value'].replace(' ', '_').lower()}"
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try:
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custom_parser = getattr(self, parser_query)
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info = custom_parser(info)
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except AttributeError:
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logger.error(f"Couldn't find submission parser: {parser_query}")
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# parser_query = f"parse_{self.sub['submission_type']['value'].replace(' ', '_').lower()}"
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# custom_parser = getattr(self, parser_query)
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# except AttributeError:
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# logger.error(f"Couldn't find submission parser: {parser_query}")
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for k,v in info.items():
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match k:
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case "sample":
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@@ -120,41 +119,41 @@ class SheetParser(object):
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"""
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self.sample_result, self.sub['samples'] = SampleParser(ctx=self.ctx, xl=self.xl, submission_type=self.sub['submission_type']['value']).parse_samples()
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def parse_bacterial_culture(self, input_dict) -> dict:
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"""
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Update submission dictionary with type specific information
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# def parse_bacterial_culture(self, input_dict) -> dict:
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# """
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# Update submission dictionary with type specific information
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Args:
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input_dict (dict): Input sample dictionary
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# Args:
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# input_dict (dict): Input sample dictionary
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Returns:
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dict: Updated sample dictionary
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"""
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return input_dict
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# Returns:
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# dict: Updated sample dictionary
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# """
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# return input_dict
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def parse_wastewater(self, input_dict) -> dict:
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"""
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Update submission dictionary with type specific information
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# def parse_wastewater(self, input_dict) -> dict:
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# """
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# Update submission dictionary with type specific information
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Args:
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input_dict (dict): Input sample dictionary
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# Args:
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# input_dict (dict): Input sample dictionary
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Returns:
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dict: Updated sample dictionary
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"""
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return input_dict
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# Returns:
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# dict: Updated sample dictionary
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# """
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# return input_dict
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def parse_wastewater_artic(self, input_dict:dict) -> dict:
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"""
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Update submission dictionary with type specific information
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# def parse_wastewater_artic(self, input_dict:dict) -> dict:
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# """
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# Update submission dictionary with type specific information
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Args:
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input_dict (dict): Input sample dictionary
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# Args:
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# input_dict (dict): Input sample dictionary
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Returns:
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dict: Updated sample dictionary
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"""
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return input_dict
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# Returns:
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# dict: Updated sample dictionary
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# """
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# return input_dict
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def import_kit_validation_check(self):
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@@ -206,6 +205,7 @@ class InfoParser(object):
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self.map = self.fetch_submission_info_map(submission_type=submission_type)
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self.xl = xl
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logger.debug(f"Info map for InfoParser: {pprint.pformat(self.map)}")
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def fetch_submission_info_map(self, submission_type:str|dict) -> dict:
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"""
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@@ -223,6 +223,8 @@ class InfoParser(object):
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# submission_type = lookup_submissiontype_by_name(ctx=self.ctx, type_name=submission_type['value'])
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submission_type = lookup_submission_type(ctx=self.ctx, name=submission_type['value'])
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info_map = submission_type.info_map
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# Get the parse_info method from the submission type specified
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self.custom_parser = get_polymorphic_subclass(models.BasicSubmission, submission_type.name).parse_info
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return info_map
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def parse_info(self) -> dict:
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@@ -263,7 +265,13 @@ class InfoParser(object):
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continue
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else:
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dicto[item] = dict(value=convert_nans_to_nones(value), parsed=False)
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return dicto
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try:
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check = dicto['submission_category'] not in ["", None]
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except KeyError:
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check = False
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return self.custom_parser(input_dict=dicto, xl=self.xl)
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class ReagentParser(object):
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@@ -351,6 +359,7 @@ class SampleParser(object):
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submission_type = lookup_submission_type(ctx=self.ctx, name=submission_type)
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logger.debug(f"info_map: {pprint.pformat(submission_type.info_map)}")
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sample_info_map = submission_type.info_map['samples']
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self.custom_parser = get_polymorphic_subclass(models.BasicSubmission, submission_type.name).parse_samples
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return sample_info_map
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def construct_plate_map(self, plate_map_location:dict) -> pd.DataFrame:
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@@ -473,12 +482,12 @@ class SampleParser(object):
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except KeyError:
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translated_dict[k] = convert_nans_to_nones(v)
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translated_dict['sample_type'] = f"{self.submission_type} Sample"
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parser_query = f"parse_{translated_dict['sample_type'].replace(' ', '_').lower()}"
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try:
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custom_parser = getattr(self, parser_query)
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translated_dict = custom_parser(translated_dict)
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except AttributeError:
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logger.error(f"Couldn't get custom parser: {parser_query}")
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# parser_query = f"parse_{translated_dict['sample_type'].replace(' ', '_').lower()}"
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# try:
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# custom_parser = getattr(self, parser_query)
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translated_dict = self.custom_parser(translated_dict)
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# except AttributeError:
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# logger.error(f"Couldn't get custom parser: {parser_query}")
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if generate:
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new_samples.append(self.generate_sample_object(translated_dict))
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else:
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@@ -502,7 +511,7 @@ class SampleParser(object):
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logger.error(f"Could not find the model {query}. Using generic.")
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database_obj = models.BasicSample
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logger.debug(f"Searching database for {input_dict['submitter_id']}...")
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instance = lookup_samples(ctx=self.ctx, submitter_id=input_dict['submitter_id'])
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instance = lookup_samples(ctx=self.ctx, submitter_id=str(input_dict['submitter_id']))
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if instance == None:
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logger.debug(f"Couldn't find sample {input_dict['submitter_id']}. Creating new sample.")
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instance = database_obj()
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@@ -516,63 +525,63 @@ class SampleParser(object):
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return dict(sample=instance, row=input_dict['row'], column=input_dict['column'])
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def parse_bacterial_culture_sample(self, input_dict:dict) -> dict:
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"""
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Update sample dictionary with bacterial culture specific information
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# def parse_bacterial_culture_sample(self, input_dict:dict) -> dict:
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# """
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# Update sample dictionary with bacterial culture specific information
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Args:
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input_dict (dict): Input sample dictionary
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# Args:
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# input_dict (dict): Input sample dictionary
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Returns:
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dict: Updated sample dictionary
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"""
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logger.debug("Called bacterial culture sample parser")
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return input_dict
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# Returns:
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# dict: Updated sample dictionary
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# """
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# logger.debug("Called bacterial culture sample parser")
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# return input_dict
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def parse_wastewater_sample(self, input_dict:dict) -> dict:
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"""
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Update sample dictionary with wastewater specific information
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# def parse_wastewater_sample(self, input_dict:dict) -> dict:
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# """
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# Update sample dictionary with wastewater specific information
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Args:
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input_dict (dict): Input sample dictionary
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# Args:
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# input_dict (dict): Input sample dictionary
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Returns:
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dict: Updated sample dictionary
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"""
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logger.debug(f"Called wastewater sample parser")
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return input_dict
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# Returns:
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# dict: Updated sample dictionary
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# """
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# logger.debug(f"Called wastewater sample parser")
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# return input_dict
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def parse_wastewater_artic_sample(self, input_dict:dict) -> dict:
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"""
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Update sample dictionary with artic specific information
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# def parse_wastewater_artic_sample(self, input_dict:dict) -> dict:
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# """
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# Update sample dictionary with artic specific information
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Args:
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input_dict (dict): Input sample dictionary
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# Args:
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# input_dict (dict): Input sample dictionary
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Returns:
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dict: Updated sample dictionary
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"""
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logger.debug("Called wastewater artic sample parser")
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input_dict['sample_type'] = "Wastewater Sample"
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# Because generate_sample_object needs the submitter_id and the artic has the "({origin well})"
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# at the end, this has to be done here. No moving to sqlalchemy object :(
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input_dict['submitter_id'] = re.sub(r"\s\(.+\)$", "", str(input_dict['submitter_id'])).strip()
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return input_dict
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# Returns:
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# dict: Updated sample dictionary
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# """
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# logger.debug("Called wastewater artic sample parser")
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# input_dict['sample_type'] = "Wastewater Sample"
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# # Because generate_sample_object needs the submitter_id and the artic has the "({origin well})"
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# # at the end, this has to be done here. No moving to sqlalchemy object :(
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# input_dict['submitter_id'] = re.sub(r"\s\(.+\)$", "", str(input_dict['submitter_id'])).strip()
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# return input_dict
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def parse_first_strand_sample(self, input_dict:dict) -> dict:
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"""
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Update sample dictionary with first strand specific information
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# def parse_first_strand_sample(self, input_dict:dict) -> dict:
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# """
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# Update sample dictionary with first strand specific information
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Args:
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input_dict (dict): Input sample dictionary
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# Args:
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# input_dict (dict): Input sample dictionary
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Returns:
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dict: Updated sample dictionary
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"""
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logger.debug("Called first strand sample parser")
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input_dict['well'] = re.search(r"\s\((.*)\)$", input_dict['submitter_id']).groups()[0]
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input_dict['submitter_id'] = re.sub(r"\s\(.*\)$", "", str(input_dict['submitter_id'])).strip()
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return input_dict
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# Returns:
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# dict: Updated sample dictionary
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# """
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# logger.debug("Called first strand sample parser")
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# input_dict['well'] = re.search(r"\s\((.*)\)$", input_dict['submitter_id']).groups()[0]
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# input_dict['submitter_id'] = re.sub(r"\s\(.*\)$", "", str(input_dict['submitter_id'])).strip()
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# return input_dict
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def grab_plates(self) -> List[str]:
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"""
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